GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ATPgrasp_Ter - ATP-grasp in the biosynthetic pathway with Ter operon
Pfam: PF15632 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0179
Length: 329
Sequences: 8777
Seq/Len: 26.68
HH_delta: 0.338 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
139_E168_R1.252613.504
117_A253_A1.203453.366
245_E249_R1.158223.240
124_P204_E1.057212.957
167_S170_E1.056742.956
248_R252_E1.054892.951
135_K172_D1.048922.934
60_D64_E1.045552.925
84_D103_E1.000932.800
84_D88_A0.966072.702
130_T133_E0.958192.680
30_H46_L0.900152.518
115_M250_L0.873372.443
126_W140_E0.859992.406
301_K306_E0.85412.389
103_E110_A0.811442.270
110_A113_E0.792712.217
241_E245_E0.792582.217
219_E257_D0.791922.215
113_E117_A0.789632.209
45_Y65_H0.761162.129
137_A140_E0.75842.121
165_D207_P0.729292.040
45_Y61_F0.721332.018
136_A140_E0.705451.973
217_A222_V0.700161.959
100_E104_L0.695011.944
143_F168_R0.690881.933
63_K89_L0.671611.879
129_R133_E0.664821.860
246_L272_P0.662911.854
98_S101_T0.661761.851
298_L309_P0.658521.842
242_E271_N0.654751.831
79_L82_H0.632631.770
170_E174_L0.632631.770
85_E89_L0.629261.760
172_D176_E0.618941.731
297_Y301_K0.605971.695
242_E245_E0.605631.694
137_A141_L0.595261.665
281_P295_L0.591061.653
25_T43_E0.589661.649
126_W137_A0.584331.635
121_P271_N0.583131.631
216_L302_L0.581691.627
104_L114_F0.580891.625
138_Y143_F0.580151.623
213_V243_L0.576591.613
86_F91_V0.575541.610
131_A135_K0.567141.586
59_L63_K0.566521.585
221_R252_E0.564091.578
249_R252_E0.5631.575
132_D136_A0.559481.565
168_R172_D0.551491.543
98_S257_D0.547331.531
87_E99_A0.546591.529
62_C70_F0.541661.515
43_E65_H0.534431.495
133_E136_A0.533031.491
135_K168_R0.527841.476
136_A139_E0.51321.436
215_C251_A0.512471.434
216_L298_L0.506781.418
112_Y203_M0.503521.408
61_F65_H0.502111.405
124_P140_E0.500281.399
113_E116_E0.498621.395
215_C247_A0.497221.391
105_A277_I0.495151.385
266_Y272_P0.490791.373
135_K139_E0.490771.373
220_G252_E0.489541.369
107_D153_A0.48451.355
109_A113_E0.48141.347
222_V248_R0.478471.338
104_L110_A0.47321.324
165_D170_E0.466521.305
163_V205_Y0.464211.299
138_Y148_L0.463571.297
62_C91_V0.461521.291
132_D135_K0.461011.290
121_P246_L0.460131.287
239_N266_Y0.458831.283
239_N242_E0.457721.280
153_A199_P0.452731.266
57_W60_D0.450741.261
86_F93_L0.448051.253
216_L259_L0.447621.252
60_D63_K0.446261.248
213_V247_A0.444661.244
78_L82_H0.442031.236
171_L174_L0.441811.236
170_E175_F0.440131.231
134_L175_F0.434741.216
236_V239_N0.432381.209
128_V137_A0.432021.208
171_L175_F0.418211.170
148_L202_V0.41671.166
133_E137_A0.416021.164
167_S171_L0.41281.155
170_E173_A0.409821.146
207_P268_E0.407381.140
215_C260_F0.404341.131
114_F118_N0.40361.129
217_A252_E0.401391.123
55_V59_L0.39971.118
114_F117_A0.399391.117
241_E244_I0.395761.107
115_M274_L0.39411.102
105_A254_F0.392541.098
116_E122_V0.391081.094
226_V229_R0.390741.093
85_E88_A0.389581.090
94_L300_V0.386161.080
237_L241_E0.385931.080
245_E248_R0.384361.075
56_D85_E0.379261.061
38_L44_A0.375151.049
101_T255_G0.371411.039
213_V244_I0.367431.028
134_L171_L0.365431.022
109_A153_A0.36341.017
221_R309_P0.361541.011
246_L264_F0.360291.008
242_E246_L0.359351.005
143_F171_L0.359271.005
59_L89_L0.358991.004
23_D29_S0.35871.003
114_F253_A0.3570.999
243_L272_P0.355940.996
204_E273_K0.354170.991
109_A127_R0.351940.984
244_I248_R0.351740.984
84_D99_A0.349710.978
92_K257_D0.346510.969
92_K219_E0.34550.966
99_A103_E0.345260.966
68_D92_K0.344790.964
82_H103_E0.343510.961
218_D221_R0.34350.961
149_C163_V0.343290.960
300_V304_L0.342890.959
36_P40_A0.342490.958
24_F304_L0.341030.954
261_N282_S0.340860.953
112_Y122_V0.339970.951
23_D28_A0.338460.947
293_V298_L0.33710.943
213_V227_P0.336850.942
132_D172_D0.335610.939
84_D100_E0.335030.937
139_E143_F0.334580.936
143_F167_S0.331120.926
227_P230_K0.329710.922
139_E167_S0.328980.920
222_V251_A0.32320.904
128_V133_E0.322150.901
169_D172_D0.318980.892
100_E110_A0.318190.890
128_V134_L0.312770.875
298_L301_K0.312370.874
104_L117_A0.310350.868
154_V197_F0.309910.867
224_A244_I0.308490.863
276_E280_R0.305540.855
232_G236_V0.303760.850
227_P231_L0.303740.850
149_C161_F0.302530.846
141_L148_L0.299250.837
249_R253_A0.298460.835
29_S47_E0.297490.832
127_R199_P0.297230.831
247_A262_I0.296240.829
208_G268_E0.295620.827
102_L279_P0.295460.826
100_E103_E0.295310.826
240_D244_I0.293420.821
169_D173_A0.291540.816
220_G307_P0.290750.813
28_A44_A0.289810.811
86_F89_L0.289720.810
28_A41_A0.289380.809
62_C86_F0.288420.807
251_A260_F0.288250.806
116_E124_P0.288070.806
247_A264_F0.286950.803
242_E249_R0.28690.803
110_A117_A0.286330.801
110_A114_F0.285870.800
135_K171_L0.284320.795
94_L303_A0.284230.795
123_P273_K0.283580.793
84_D87_E0.281220.787
118_N253_A0.281160.786
131_A176_E0.280770.785
108_K151_K0.278720.780
81_A99_A0.278210.778
131_A172_D0.278140.778
75_N78_L0.277690.777
87_E100_E0.276680.774
229_R233_R0.276480.773
131_A175_F0.276210.773
149_C205_Y0.274860.769
164_L174_L0.274640.768
46_L49_A0.272970.764
121_P273_K0.272380.762
247_A251_A0.271160.758
47_E61_F0.270060.755
231_L235_Q0.269890.755
173_A189_A0.269010.752
233_R236_V0.268480.751
131_A134_L0.268410.751
61_F67_I0.26810.750
104_L253_A0.267920.749
221_R307_P0.267210.747
215_C262_I0.266910.747
66_G89_L0.266830.746
87_E257_D0.264940.741
98_S219_E0.263850.738
175_F200_L0.263430.737
222_V252_E0.263150.736
229_R232_G0.262390.734
211_Y266_Y0.261670.732
120_I246_L0.26050.729
120_I249_R0.259970.727
148_L164_L0.25970.726
150_V202_V0.257570.720
161_F230_K0.257550.720
214_D284_G0.256640.718
251_A262_I0.256330.717
261_N284_G0.255930.716
225_A229_R0.255930.716
262_I277_I0.255830.716
30_H49_A0.255410.714
268_E271_N0.254670.712
114_F254_F0.254020.711
27_I47_E0.253460.709
135_K138_Y0.253320.709
129_R199_P0.253070.708
233_R237_L0.251510.704
158_G276_E0.251080.702
98_S255_G0.249630.698
63_K85_E0.249370.698
261_N283_G0.248030.694
165_D168_R0.247940.694
242_E272_P0.247470.692
164_L167_S0.247470.692
134_L137_A0.246430.689
125_Y203_M0.246230.689
232_G235_Q0.245690.687
207_P269_D0.245670.687
70_F91_V0.243490.681
159_R190_A0.242910.679
87_E98_S0.241610.676
150_V200_L0.241110.674
301_K309_P0.240350.672
227_P232_G0.238930.668
25_T42_D0.238350.667
215_C222_V0.238280.667
167_S172_D0.237890.665
246_L249_R0.23730.664
45_Y64_E0.237010.663
112_Y116_E0.236050.660
69_V72_P0.235550.659
206_L273_K0.23540.658
112_Y125_Y0.235040.657
266_Y271_N0.233960.654
59_L85_E0.233870.654
234_R237_L0.233270.653
214_D261_N0.232970.652
214_D283_G0.232740.651
131_A171_L0.232620.651
173_A176_E0.232570.651
218_D308_I0.231530.648
70_F86_F0.230480.645
204_E271_N0.230110.644
27_I65_H0.229950.643
31_R49_A0.229440.642
47_E57_W0.229150.641
227_P235_Q0.229080.641
78_L81_A0.228930.640
263_Q282_S0.22890.640
115_M122_V0.228870.640
238_E242_E0.22880.640
238_E241_E0.228780.640
250_L262_I0.22790.637
59_L91_V0.225920.632
226_V232_G0.224550.628
71_V299_A0.2240.627
27_I45_Y0.222450.622
210_E282_S0.221880.621
27_I61_F0.221560.620
138_Y142_R0.221150.619
29_S61_F0.220810.618
217_A260_F0.21990.615
123_P204_E0.218970.613
108_K276_E0.218680.612
218_D305_G0.218550.611
227_P233_R0.218130.610
210_E214_D0.218020.610
217_A257_D0.21790.610
189_A192_Q0.217670.609
225_A231_L0.217390.608
226_V230_K0.21630.605
227_P234_R0.216140.605
257_D302_L0.215820.604
107_D110_A0.21560.603
114_F250_L0.215360.602
55_V85_E0.215330.602
251_A254_F0.214810.601
59_L62_C0.214230.599
115_M118_N0.213840.598
127_R153_A0.213650.598
59_L88_A0.212470.594
68_D304_L0.212250.594
203_M206_L0.211850.593
58_C62_C0.211840.593
167_S175_F0.211530.592
230_K233_R0.211430.591
137_A202_V0.211190.591
63_K66_G0.211130.591
256_L260_F0.21060.589
115_M120_I0.210550.589
62_C67_I0.20970.587
24_F224_A0.208910.584
107_D199_P0.208820.584
105_A250_L0.20830.583
134_L202_V0.206720.578
296_P300_V0.206720.578
172_D175_F0.20650.578
150_V164_L0.204550.572
208_G269_D0.204110.571
76_R79_L0.20410.571
100_E255_G0.203750.570
101_T104_L0.20330.569
154_V198_P0.202690.567
135_K167_S0.202230.566
231_L236_V0.201980.565
245_E252_E0.201480.564
111_F277_I0.201450.564
58_C61_F0.201390.563
130_T136_A0.201220.563
62_C66_G0.20040.561
281_P296_P0.200280.560
214_D282_S0.199990.559
36_P39_Y0.199750.559
202_V205_Y0.199620.558
250_L254_F0.199180.557
216_L293_V0.198630.556
46_L57_W0.198280.555
153_A197_F0.197650.553
230_K235_Q0.19670.550
25_T126_W0.196520.550
101_T257_D0.196280.549
138_Y171_L0.196140.549
210_E263_Q0.196060.548
241_E248_R0.195940.548
205_Y208_G0.195820.548
263_Q283_G0.195180.546
61_F64_E0.194740.545
150_V174_L0.194550.544
225_A230_K0.194080.543
108_K111_F0.193440.541
123_P275_L0.193150.540
236_V270_G0.193060.540
156_I282_S0.192770.539
69_V92_K0.192610.539
266_Y270_G0.192170.538
111_F153_A0.192080.537
109_A112_Y0.191950.537
217_A248_R0.191860.537
135_K143_F0.191860.537
250_L274_L0.191830.537
63_K88_A0.191730.536
63_K91_V0.19160.536
79_L83_R0.190960.534
285_I289_C0.190550.533
30_H35_A0.19050.533
101_T105_A0.190440.533
226_V231_L0.190360.532
25_T29_S0.190230.532
56_D63_K0.190040.532
105_A256_L0.18970.531
288_S295_L0.189450.530
120_I274_L0.18930.530
287_Y290_A0.18830.527
106_D111_F0.188120.526
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
2pn1A0.91191000.338
4dimA0.9241000.36
1a9xA0.92711000.361
3ouzA0.95441000.362
3u9tA0.95441000.363
3n6rA0.95441000.367
3votA0.95441000.367
3glkA0.94221000.367
3hblA0.95141000.372
3jrxA0.94221000.374

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